Single nucleotide polymorphisms associated with bull fertility

ABSTRACT

Single nucleotide polymorphic sites of the bovine MAP1B, PPP1R11, and DDX4 genes are associated with improved bull fertility as measured by e.g. sire conception rates. Nucleic acid molecules, arrays, kits, methods of genotyping and marker-assisted bovine breeding methods based on these SNPs are disclosed.

CROSS-REFERENCE TO RELATED APPLICATION

This is a divisional application of U.S. application Ser. No. 13/798,181filed on Mar. 13, 2013, claiming priority to U.S. Patent Application61/681,152, filed on Aug. 9, 2012, the entire disclosure of which isincorporated herein by reference.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with government support under 12-CRHF-0-6055awarded by the USDA/NIFA. The government has certain rights in theinvention.

FIELD OF THE INVENTION

The present invention relates to compositions and methods for testingand selecting cattle using molecular genetic methods by assaying for thepresence of at least one genetic marker indicative of increased bullfertility. Specifically, genetic variations in the MAP1B and PPP1R11genes are tested and used for selecting cattle animals with improvedblastocyst or fertilization rates, or both.

BACKGROUND OF THE INVENTION

The dairy cattle genome has been significantly restructured over thepast 30 years due to intensive breeding effort selecting for productiontraits, including high quality milk and high and sustained productivity.However, while those efforts led to dramatic improvement ofproductivity, there has been significant reproductive deterioration inhigh-producing dairy cows, which in turn has caused substantial economicloss in the dairy cattle industry (Lucy, 2007, Fertility inhigh-producing dairy cows: reasons for decline and corrective strategiesfor sustainable improvement. Society of Reproduction and FertilitySupplement. 64 237-254). Key factors contributing to decreasingfertility of dairy cow are low fertilization rates and decreasedembryonic survival.

Fertility is a complex trait that comprises developmental stages such ascombining sperm and egg to form a zygote, compaction of embryo cells toform a morula, establishment of the blastocyst, attachment of the embryoto the uterus, and fetal development (Amann and DeJarnette, 2012). Thiscomplexity makes accurate prediction of successful pregnancy difficult,as aberrant development of sperm, oocyte, embryo, or fetus all wouldlead to conception failure. Conception rate in dairy cattle is about40%, and only 50% of the fertilized eggs produce viable embryos (Santoset al., 2004). The decline in reproductive performance in cattle overthe past few decades (Dobson et al., 2007) has been ascribed primarilyto fertilization failure and early embryonic loss (Santos et al., 2004).

Previous studies have shown that genetic makeup of an individual playscrucial roles in embryonic development and reproductive success (Weigel,2006; Shook, 2006). Although a male and female parent each contributeshalf of its genetic material to the new zygote and both are necessaryfor embryo development, it is not obvious whether or not thiscontribution is equally important to pregnancy success. For example, itis well established that the paternal genome supports growth ofextra-embryonic tissues while the maternal genome fosters development ofthe embryo proper (Barton et al., 1984). After fertilization, thedevelopment of an embryo is controlled by maternal genomic informationthat is accumulated during oogenesis (Telford et al., 1990). It is onlyat the 8-cell stage in the bovine embryo that the embryonic genomeactivates and the embryo switches to transcribing its own RNA (Memiliand First, 2000).

Despite that most breeding schemes in cattle are focused on theselection of elite bulls using progeny testing or genomic selection, andthat some semen traits (e.g., sperm motility and percentage of abnormalsperm) show moderate to high heritabilities (Druet et al., 2009), mostfertility studies in cattle have focused on the maternal contribution,and the paternal contribution to reproductive performance has not beenthoroughly investigated, and only a few studies have been reported inthe literature (Feugang et al., 2009; Khatib et al., 2010; Peñagaricanoet al., 2012). Therefore, characterization of bull fertility markers isboth feasible and highly desirable, and the deployment of these markersin cattle breeding would lead to improved reproductive performance incattle.

A recent comparative genomics study has characterized many genesinvolved in the control of spermatogenesis that were highly conservedfrom fly to human (Bonilla and Xu, 2008). Some of these genes werereported to be crucial for human fertility. However, it is not knownwhether or not these spermatogenesis genes play important roles in thefertility of bulls.

SUMMARY OF THE INVENTION

The present inventor carried out an association analysis between highlyconserved spermatogenesis genes and sire conception rate (SCR) as ameasure of bull fertility, with the objective that significantpolymorphisms associated with bull fertility can be used as geneticmarkers in breeding programs aimed at improving reproductive performancein cattle.

Specifically, an association analysis is performed between highlyconserved spermatogenesis genes and SCR in US Holstein populations as ameasure of bull fertility. Sequence analysis revealed 24 singlenucleotide polymorphisms (SNPs) in 9 genes in the bull population usingthe pooled DNA sequencing approach. These 9 genes were selected fortheir high level of sequence conservation between flies and humans.Overall, the 24 SNPs were tested for association with SCR in apopulation of 1,988 bulls. Three SNPs located in the MAP1B gene, one SNPin the PPP1R11 gene and one SNP in the DDX4 gene showed significantassociations with SCR. Nucleotide probes based upon these SNPs are foundto be useful for genetic testing of bull animals for improvedfertilization rate.

Accordingly, in one embodiment, the present invention provides anisolated oligo- or poly-nucleotide molecule consisting of

-   -   1) a nucleotide of Position 3066 of SEQ ID NO:1 and at least 12,        but not more than 200 contiguous nucleotides of FIG. 1 adjacent        to position 3066;    -   2) Position 3323 of SEQ ID NO:1 and at least 12, but not more        than 200 contiguous nucleotides of FIG. 1 adjacent to position        3323;    -   3) Position 87071 of SEQ ID NO:2 and at least 12, but not more        than 200 contiguous nucleotides of FIG. 3 adjacent to position        87071,    -   (4) Position 112 of SEQ ID NO:3 and at least 12, but not more        than 200 contiguous nucleotides of SEQ ID NO:3 adjacent to        position 112,    -   (5) Position 61646 of SEQ ID NO:4 and at least 12, but not more        than 200 contiguous nucleotides of FIG. 6 adjacent to position        61646, and    -   6) Position 34239 of SEQ ID NO:5 and at least 12, but not more        than 200 contiguous nucleotides of FIG. 5 adjacent to position        61646.

In one embodiment, the nucleotide molecule of the present inventioncomprises at least about 15 contiguous nucleotides adjacent to itsrespective position (hereinafter the “SNP position”) of the respectivefigure. In one embodiment, the nucleic acid molecule of the presentinvention comprises at least about 20 contiguous nucleotides adjacent tothe respective SNP position. In one embodiment, the oligonucleotidemolecule of the present invention consists of not more than about 100nucleotides. In one embodiment, the oligonucleotide molecule of thepresent invention consists of not more than about 50 nucleotides. In oneembodiment, the SNP position of the nucleotide molecule of the presentinvention near or at the center of the molecule; alternatively, the SNPposition is at the 3′-end of the oligonucleotide molecule.

Also provided herein is an array of nucleic acid molecules, comprisingthe isolated oligonucleotide molecule of the present invention,supported on a substrate. The substrate may be any suitable medium,known and readily available to one of ordinary skills in the art, andthe array may be addressable.

The present invention further provides a kit comprising an isolatedoligonucleotide molecule of the present invention, and a suitablecontainer.

In another embodiment, the present invention provides a method fordetecting single nucleotide polymorphism (SNP) in a gene listed in Table1 below in a bovine cell, the method comprising optionally isolating anDNA from the bovine cell, determining the identity of a nucleotide onthe gene of the cell at a SNP position identified in Table 1 below, andcomparing the identity to the preferred nucleotide identity at acorresponding position in Table 1.

In one embodiment, the bovine cell may be an adult cell, an embryo cell,a sperm, an egg, a fertilized egg, or a zygote. The identity of thenucleotide may be determined by many methods known and readily availableto those ordinarily skilled in the art, such as but not limited tosequencing a nucleic acid molecule comprising a suitable portion of thegene of the cell comprising a respective SNP position, or by hybridizinga suitable probe to a nucleic acid preparation from the cell, whichprobe may be suitably labeled e.g. fluorescently or radioactively.

The nucleic acid molecule may be isolated from the cell via a largevariety of methods, known and readily available to an ordinarily skilledartisan, such as amplification by the polymerase chain reaction (PCR) ofgenomic DNA of the cell, or when appropriate, by RT-PCR of the mRNA ofthe cell.

In preferred embodiment, both copies of the gene in a diploid genome aregenotyped according to the method of the present invention.

The identity of the nucleotide may be determined based on genotypes ofthe parent of the cell, genotypes of the daughter of the cell, or both,through genetic analysis methods well-known to those skilled in the art.

A method is further provided for determining whether an individualbovine animal is suitable as a gamete donor for natural mating,artificial insemination or in vitro fertilization, the method comprisingdetecting the SNP according to the above method of the presentinvention, and excluding as gamete donor an individual which does nothave the preferred allele identity at the respective SNP position asdescribed in Table 1.

In one embodiment, the individual is excluded as a gamete donor if theindividual, whose genotype is not homozygous of the preferred allelewith regard to the respective SNP position.

The present invention additionally provides a method of selecting abovine embryo for planting in a uterus, the method comprising genotypingthe embryo according to the present invention, while preserving theviability of the embryo, and excluding from planting an embryo whichdoes not have the preferred allele identity at the respective SNPposition as described in Table 1.

In another embodiment, the present invention further provides a methodfor selectively breeding cattle using a multiple ovulation and embryotransfer procedure (MOET), the method comprising superovulating a femaleanimal, collecting eggs from said superovulated female, in vitrofertilizing said eggs from a male animal which has at least onepreferred allele identity at the respective SNP position as described inTable 1, implanting said fertilized eggs into other females allowing foran embryo to develop.

In another embodiment, the method for selectively breeding cattle usingMOET may further comprise a step of genotyping the male animal accordingto the method of the present invention.

In another embodiment, the method for selectively breeding cattle usingMOET may further comprise a step of genotyping the developing embryo,and allowing pregnancy to proceed only if the genotype of the embryocomprises at least one preferred allele identity at the respective SNPposition as described in Table 1.

DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a partial genomic sequence of MAP1B, showing thelocations of SNPs 1, 2 and 3 on the MAP1B gene and the locations of theprimers (1F and 1R, corresponding to positions 2859-2876, and positions3346-3362, respectively) used to amplify the region comprising the SNPsites. The numbering of the sequences is according to that of GenBankAccession No. (Gene ID: 514739, updated on 12 Jul. 2012), incorporatedherein by reference in its entirety.

FIG. 2 is the partial genomic sequence of the MAP1B gene showing thelocations of SNPs 4 and 6 on the MAP1B gene and the locations of theprimers 2F and 2R (corresponding to positions 51447-51466, and positions51931-51948, respectively used to amplify the region comprising the SNPsites. The numbering of the sequence is according to that of GenBankAccession No. (Gene ID: 514739, updated on 12 Jul. 2012), incorporatedherein by reference in its entirety.

FIG. 3 is the partial genomic sequence of the MAP1B gene showing thelocation of SNP 5 on the MAP1B gene and the locations of the primers 3Fand 3R (corresponding to positions 86634-86651, and positions87260-87278, respectively) used to amplify the region comprising the SNPsites. The numbering of the sequence is per that of GenBank AccessionNo. (Gene ID: 514739), incorporated herein by reference in its entirety.

FIG. 4. is the partial genomic sequence of the PPP1R11 gene showing thelocations of SNPs 1-4 on the PPPiR11 gene and the locations of theprimers 1F and 1R (corresponding to positions −102 to −85, and positions470-489, respectively) used to amplify the region comprising the SNPsites. The numbering of the sequences is according to GenBank AccessionNo. (Gene ID: 504846), incorporated herein by reference in its entirety.

FIG. 5 is the partial genomic sequence of the DDX4 gene, showing thelocation of SNP 2 on the DDX4 gene and the locations of the primers 1Fand 1R (corresponding to positions 34014-34031, and positions34398-34417, respectively) used to amplify the region comprising the SNPsite. The numbering of the sequences is according to that of GenBankAccession No. (Gene ID: 493725), incorporated herein by reference in itsentirety.

FIG. 6 is the partial genomic sequence of the DDX4 showing the locationof SNP 1 on the DDX4 gene and the locations of the primers 2F and 2R(corresponding to positions 61531-61549, and positions 61867-61884,respectively) used to amplify the region comprising the SNP site. Thenumber of the sequences is per that of GenBank Accession No. (Gene ID:493725), incorporated herein by reference in its entirety.

DETAILED DESCRIPTION OF THE INVENTION

The present inventor has found that the spermatogenesis genes MAP1B,PPP1R11 and DDX4 showed significant associations with SCR. Table 1 belowsummarizes the SNPs demonstrated to be significantly associated withsire conception rates according to the present invention.

TABLE 1 Genetic markers significantly associated with sire conceptionrate Nucleotide Nucleotide Identity of Identity of Preferred PolymorphSNP ID Location/Position Allele in GenBank SNP1.MAP1B Position 3066 ofFIG. 1 A A SNP3.MAP1B Position 3323 of FIG. 1 T T SNP5.MAP1B Position87071 of FIG. 3 C C SNP1.PPP1R11 Position 112 of FIG. 4 G T SNP1.DDX4Position 61646 of FIG. 6 A A SNP2.DDX4 Position 34239 of FIG. 5 G G

Three SNPs in MAP1B, in low to moderate linkage disequilibrium (LD),were significantly associated with SCR. After correction for multipletesting, only one SNP in intron 5, SNP 5, showed the most significantassociation with SCR.

The MAR1B gene belongs to the microtubule-associated protein family andis known to affect neuronal development such as axon growth (Tymanskyjet al., 2012), development of dendritic spine and synaptic maturation(Tortosa et al., 2011), and regulation of the interaction betweenmicrotubules and actin microfilaments for axonal development(Montenegro-Venegas et al., 2010). Recent reports on the expression ofMAP1B in the male reproductive tract in both rat and human (Queiróz etal., 2006) and in testis of fruit fly and mouse (Bonilla and Xu, 2008)suggest important functions of this gene in the regulation of malefertility. The finding by the present inventor, disclosed herein, thatthe MAP1B gene is associated with SCR, supports the conclusion thatMAP1B plays a role in male fertility across a wide range of species.

The present inventor also found that a SNP in the 5′UTR of PPP1R11 wasassociated with SCR in the bull population examined in this study. Thisis the first report of association between male fertility in cattle andPPP1R11, which is consistent with previous reports on the roles of thisgene in spermatogenesis in mouse and human. For example, the differentisoforms of PPP1R11 (also known as TCTEX5) were found to be expressed inmost mouse tissues with high expression in testis, epididymis, and inthe head and tail regions of spermatozoa (Han et al., 2007). In asubsequent study, it was shown that mutations in the long transcript ofPPP1R11 were associated with normal sperm function (Han et al., 2008).The authors concluded that PPP1R11 plays important roles in spermmotility and spermatogenesis. A recent study reported that an isoform ofprotein phosphatase 1 (PP1γ 2), which has an essential role inspermatogenesis, forms a complex with PPP1R11 in the testis (Cheng etal., 2009). Given that PP1γ 2 is regulated by PPP1R11, these resultsfurther support the idea that PPP1R11 has important functions inspermatogenesis.

The spermatogenesis genes investigated in this study were selected froma pool of genes whose expression is highly conserved in testis of bothfruit fly and mouse (Bonilla and Xu, 2008). The protein sequenceidentities between cattle and human and between cattle and fly are 91%and 32%, respectively for MAP1B and 99% and 47%, respectively forPPP1R11. As such, the association of these genes with bull fertilitytestifies to the usefulness of the comparative genomics approach inselecting candidate male fertility genes.

To further explore involvement of male fertility genes identified inthis study in female fertility, we tested the association of the SNPs inMAP1B, with fertilization and embryo survival rates using data from theIVF system. MAP1B genotypes of the cows, from which oocytes wereextracted and used for fertilization and embryo culture, weresignificantly associated with differential fertilization rate and embryosurvival rate. Recently, the expression of MAP1B was found to bedownregulated in follicular cystic follicles compared to normalfollicles, suggesting that alteration in MAP1B expression may beinvolved in reproduction failure in cattle (Choe et al., 2010). Theinstant disclosure again demonstrates the significance of both parentalgenomes to embryonic development and fertility.

Accordingly, the present invention provides nucleic acid-based geneticmarkers for identifying bovine animals, especially bulls, with superiorfertility, specifically, sire conception rate as a measure of malefertility. In general, for use as markers, isolated oligonucleotide orpolynucleotide molecules, or isolated nucleic acid fragments, preferablyDNA fragments, as used. Such markers will be of at least 10 nucleotides(nt), preferably at least 11, 12, or 15 nt, usually at least 20 nt,often at least 50 nt. Such small DNA fragments are useful as primers forthe polymerase chain reaction (PCR), and probes for hybridizationscreening, etc.

In one embodiment, the isolated nucleic acid molecule comprises not morethan 1,500 nt, or not more than 1000 nt, or not more than 900 nt, or notmore than 800 nt, or not more than 700 nt, or not more than 600 nt, ornot more than 500 nt, or not more than 400 nt, or not more than 300 nt,or not more than 200 nt., or not more than 150 nt., or not more than 100nt., or not more than 75 nt.

In the context of the present invention, the term “isolated” refers to anucleic acid molecule purified to some degree from endogenous materialswith which the nucleic acid molecule may naturally occur or exist. Atthe least, the term “isolated” refers to a nucleic acid moleculeseparated from chromatin or other protein or components of the genomicDNA. Preferably, the isolated oligonucleic acid molecule or polynucleicacid molecule of the present invention comprises a fragment that isshorter than that which is naturally occurring.

In the context of the present invention, the provided sequences alsoencompass the complementary sequence corresponding to any of theprovided polymorphisms. Where appropriate, and in order to provide anunambiguous identification of the specific site of a polymorphism, thenumbering of the original nucleic sequences in the GenBank may be used;alternatively, the numbering may simply refer to the specific sequencein the Sequence Listing accompanying this disclosure.

The term primer refers to a single-stranded oligonucleotide capable ofacting as a point of initiation of template-directed DNA synthesis underappropriate conditions (i.e., in the presence of four differentnucleoside triphosphates and an agent for polymerization, such as, DNAor RNA polymerase or reverse transcriptase) in an appropriate buffer andat a suitable temperature. The appropriate length of a primer depends onthe intended use of the primer but typically ranges from 15 to 30nucleotides. Short primer molecules generally require coolertemperatures to form sufficiently stable hybrid complexes with thetemplate. A primer need not reflect the exact sequence of the templatebut must be sufficiently complementary to hybridize with a template. Theterm primer site, or priming site, refers to the area of the target DNAto which a primer hybridizes. The term primer pair means a set ofprimers including a 5′ upstream primer that hybridizes with the 5′ endof the DNA sequence to be amplified and a 3′, downstream primer thathybridizes with the complement of the 3′ end of the sequence to beamplified. One of these two primers is often referred to as the “forwardprimer,” while the other the “reverse primer.”

The term “probe” or “hybridization probe” denotes a defined nucleic acidsegment (or nucleotide analog segment) which can be used to identify byhybridization a specific polynucleotide sequence present in samples,said nucleic acid segment comprising a nucleotide sequence complementaryof the specific polynucleotide sequence to be identified. “Probes” or“hybridization probes” are nucleic acids capable of binding in abase-specific manner to a complementary strand of nucleic acid.

An objective of the present invention is to determine which embodimentof the polymorphisms a specific sample of DNA has. For example, it isdesirable to determine whether the nucleotide at a particular positionis A or G. An oligonucleotide probe can be used for such purpose.Preferably, the oligonucleotide probe will have a detectable label, andcontains an A at the corresponding position. Experimental conditions canbe chosen such that if the sample DNA contains an A, they hybridizationsignal can be detected because the probe hybridizes to the correspondingcomplementary DNA strand in the sample, while if the sample DNA containsa G, no hybridization signal is detected.

Similarly, PCR primers and conditions can be devised, whereby theoligonucleotide is used as one of the PCR primers, for analyzing nucleicacids for the presence of a specific sequence. These may be directamplification of the genomic DNA, or RT-PCR amplification of the mRNAtranscript of the gene of interest. The use of the polymerase chainreaction is described in Saiki et al. (1985) Science 230:1350-1354.Amplification may be used to determine whether a polymorphism ispresent, by using a primer that is specific for the polymorphism.Alternatively, various methods are known in the art that utilizeoligonucleotide ligation as a means of detecting polymorphisms, forexamples see Riley et al (1990) Nucleic Acids Res. 18:2887-2890; andDelahunty et al (1996) Am. J. Hum. Genet. 58:1239-1246. The detectionmethod may also be based on direct DNA sequencing, or hybridization, ora combination thereof. Where large amounts of DNA are available, genomicDNA is used directly. Alternatively, the region of interest is clonedinto a suitable vector and grown in sufficient quantity for analysis.The nucleic acid may be amplified by PCR, to provide sufficient amountsfor analysis.

Hybridization may be performed in solution, or such hybridization may beperformed when either the oligonucleotide probe or the targetpolynucleotide is covalently or noncovalently affixed to a solidsupport. Attachment may be mediated, for example, by antibody-antigeninteractions, poly-L-Lys, streptavidin or avidin-biotin, salt bridges,hydrophobic interactions, chemical linkages, UV cross-linking baking,etc. Oligonucleotides may be synthesized directly on the solid supportor attached to the solid support subsequent to synthesis. Solid-supportssuitable for use in detection methods of the invention includesubstrates made of silicon, glass, plastic, paper and the like, whichmay be formed, for example, into wells (as in 96-well plates), slides,sheets, membranes, fibers, chips, dishes, and beads. The solid supportmay be treated, coated or derivatized to facilitate the immobilizationof the allele-specific oligonucleotide or target nucleic acid. Forscreening purposes, hybridization probes of the polymorphic sequencesmay be used where both forms are present, either in separate reactions,spatially separated on a solid phase matrix, or labeled such that theycan be distinguished from each other.

Hybridization may also be performed with nucleic acid arrays andsubarrays such as described in WO 95/11995. The arrays would contain abattery of allele-specific oligonucleotides representing each of thepolymorphic sites. One or both polymorphic forms may be present in thearray. Usually such an array will include at least 2 differentpolymorphic sequences, i.e. polymorphisms located at unique positionswithin the locus, and may include all of the provided polymorphisms.Arrays of interest may further comprise sequences, includingpolymorphisms, of other genetic sequences, particularly other sequencesof interest. The oligonucleotide sequence on the array will usually beat least about 12 nt in length, may be the length of the providedpolymorphic sequences, or may extend into the flanking regions togenerate fragments of 100 to 200 nt in length. For examples of arrays,see Ramsay (1998) Nat. Biotech. 16:4044; Hacia et al. (1996) NatureGenetics 14:441-447; Lockhart et al. (1996) Nature Biotechnol.14:1675-1680; and De Risi et al. (1996) Nature Genetics 14:457-460.

The identity of polymorphisms may also be determined using a mismatchdetection technique, including but not limited to the RNase protectionmethod using riboprobes (Winter et al., Proc. Natl. Acad. Sci. USA82:7575, 1985; Meyers et al., Science 230:1242, 1985) and proteins whichrecognize nucleotide mismatches, such as the E. coli mutS protein(Modrich, P. Ann. Rev. Genet. 25:229-253, 1991). Alternatively, variantalleles can be identified by single strand conformation polymorphism(SSCP) analysis (Orita et al., Genomics 5:874-879, 1989; Humphries etal., in Molecular Diagnosis of Genetic Diseases, R. Elles, ed., pp.321-340, 1996) or denaturing gradient gel electrophoresis (DGGE)(Wartell et al., Nucl. Acids Res. 18:2699-2706, 1990; Sheffield et al.,Proc. Natl. Acad. Sci. USA 86:232-236, 1989).

A polymerase-mediated primer extension method may also be used toidentify the polymorphism(s). Several such methods have been describedin the patent and scientific literature and include the “Genetic BitAnalysis” method (WO92/15712) and the ligase/polymerase mediated geneticbit analysis (U.S. Pat. No. 5,679,524). Related methods are disclosed inWO91/02087, WO90/09455, WO95/17676, U.S. Pat. No. 5,302,509, and U.S.Pat. No. 5,945,283. Extended primers containing a polymorphism may bedetected by mass spectrometry as described in U.S. Pat. No. 5,605,798.Another primer extension method is allele-specific PCR (Ruao et al.,Nucl. Acids Res. 17:8392, 1989; Ruao et al., Nucl. Acids Res. 19,6877-6882, 1991; WO 93/22456; Turki et al., J. Clin. Invest.95:1635-1641, 1995). In addition, multiple polymorphic sites may beinvestigated by simultaneously amplifying multiple regions of thenucleic acid using sets of allele-specific primers as described inWallace et al. (WO 89/10414).

A detectable label may be included in an amplification reaction.Suitable labels include fluorochromes, e.g. fluorescein isothiocyanate(FITC), rhodamine, Texas Red, phycoerythrin, allophycocyanin,6-carboxyfluorescein (6-FAM),2′,7′-dimethoxy-4′,5′-dichloro-6-carboxyfluorescein (JOE),6-carboxy-X-rhodamine (ROX),6-carboxy-2′,4′,7′,4,7-hexachlorofluorescein (HEX), 5-carboxyfluorescein(5-FAM) or N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA), radioactivelabels, e.g. ³²P, ³⁵S, ³H; etc. The label may be a two stage system,where the amplified DNA is conjugated to biotin, haptens, etc. having ahigh affinity binding partner, e.g. avidin, specific antibodies, etc.,where the binding partner is conjugated to a detectable label. The labelmay be conjugated to one or both of the primers. Alternatively, the poolof nucleotides used in the amplification is labeled, so as toincorporate the label into the amplification product.

It is readily recognized by those ordinarily skilled in the art that inorder to maximize the signal to noise ratio, in probe hybridizationdetection procedure, the polymorphic site should at the center of theprobe fragment used, whereby a mismatch has a maximum effect ondestabilizing the hybrid molecule; and in a PCR detection procedure, thepolymorphic site should be placed at the very 3′-end of the primer,whereby a mismatch has the maximum effect on preventing a chainelongation reaction by the DNA polymerase. The location of nucleotidesin a polynucleotide with respect to the center of the polynucleotide aredescribed herein in the following manner. When a polynucleotide has anodd number of nucleotides, the nucleotide at an equal distance from the3′ and 5′ ends of the polynucleotide is considered to be “at the center”of the polynucleotide, and any nucleotide immediately adjacent to thenucleotide at the center, or the nucleotide at the center itself isconsidered to be “within 1 nucleotide of the center.” With an odd numberof nucleotides in a polynucleotide any of the five nucleotides positionsin the middle of the polynucleotide would be considered to be within 2nucleotides of the center, and so on. When a polynucleotide has an evennumber of nucleotides, there would be a bond and not a nucleotide at thecenter of the polynucleotide. Thus, either of the two centralnucleotides would be considered to be “within 1 nucleotide of thecenter” and any of the four nucleotides in the middle of thepolynucleotide would be considered to be “within 2 nucleotides of thecenter,” and so on.

In some embodiments, a composition contains two or more differentlylabeled oligonucleotides for simultaneously probing the identity ofnucleotides or nucleotide pairs at two or more polymorphic sites. It isalso contemplated that primer compositions may contain two or more setsof allele-specific primer pairs to allow simultaneous targeting andamplification of two or more regions containing a polymorphic site.

Alternatively, the relevant portion of the gene of the sample ofinterest may be amplified via PCR and directly sequenced, and thesequence be compared to the will type sequence shown in the figures. Itis readily recognized that, other than those disclosed specificallyherein, numerous primers can be devised to achieve the objectives. PCRand sequencing techniques are well known in the art and reagents andequipments are readily available commercially.

Alternatively, an invasive signal amplification assay, as described ine.g. U.S. Pat. No. 5,422,253 and Lyamichev et al., 2000, Biochemistry39:9523-9532, both incorporated herein by reference in their entirety,may be used for detecting the SNP of interest. This assay takesadvantage of enzymes such as the 5′ nuclease activity of a DNApolymerase or the gene 6 product from bacteriophage T7 in their abilityto cleave polynucleotide molecules by recognizing specific structuresinstead of specific sequences. A single-stranded target molecule isannealed to a pilot oligonucleotide such that the 5′ end of the pilotforms a duplex with the target molecule. If the 3′ end of the pilotoligonucleotide does not pair with the target, a 3′ arm is formed. Whenexposed to a cleavage agent such as a DNA polymerase having a 5′nuclease activity or the gene 6 product from bacteriophage T7, thetarget molecule is cleaved in the 5′ region, one nucleotide into theduplex adjacent to the unpaired region of the target. If a cut in adouble-stranded molecule is required, the double-stranded molecule isdenatured. Because this unpaired 3′ arm can be as short as onenucleotide, this assay can be used for detecting a single-nucleotidedifference, e.g. in the context of SNP detection. The pilotoligonucleotide is designed such that it pairs perfectly with oneallele, but has a 3′, single nucleotide mismatch with another allele.Cleavage only occurs if there is a mismatch between the target moleculeand the pilot. To achieve signal amplification, the above invasivereaction is modified such that cleavage occurs on the pilotoligonucleotide. Two oligonucleotides are annealed in an adjacent mannerto the target molecule. The resulting adjacent duplexes overlaps by atleast one nucleotide to create an efficient substrate, called theoverlapping substrate, for the 5′ nucleases. The 5′ end of thedownstream oligonucleotide, also called the probe, contains an unpairedregion termed the 5′ arm (Lyamichev et al., 1993, Science 260:778-783.)or flap (Harrington and Lieber, 1994, EMBO J 13: 1235-1246) that is notrequired for the enzyme activity; however, very long arms can inhibitcleavage (Lyamichev et al., 1993, Science 260:778-783). Specificcleavage of the probe, termed invasive cleavage (Lyamichev et al., 1999,Nat. Biotechnol. 17 292-296; Kwiatkowski et al., 1999, Mol. Diagn. 4,353-364.), occurs at the position defined by the 3′ end of the upstreamoligonucleotide, which displaces or “invades” the probe. If the overlapbetween the adjacent oligonucleotides is only one nucleotide, cleavagetakes place between the first two base pairs of the probe, thusreleasing its 5′ arm and one nucleotide of the base paired region(Lyamichev et al., 1999, Proc. Natl. Acad. Sci. USA. 96: 6143-6148, andKaiser et al., 1999, J Biol. Chem. 274:21387-21394). if the upstreamoligonucleotide and the probe are present in large molar excess over thetarget nucleic acid, and invasive cleavage is carried out near themelting temperature of the probe, a cut probe can rapidly dissociate,and an intact probe will anneal to the target more frequently than willa cut probe, thus initiating a new cycle of cleavage. This allowsmultiple probes to be cut for each target molecule under isothermalconditions, resulting in linear signal amplification with respect totarget concentration and time (Lyamichev et al., 1999, Nat. Biotechnol.17: 292-296).

DNA markers have several advantages; segregation is easy to measure andis unambiguous, and DNA markers are co-dominant, i.e., heterozygous andhomozygous animals can be distinctively identified. Once a marker systemis established selection decisions could be made very easily, since DNAmarkers can be assayed any time after a blood sample can be collectedfrom the individual infant animal, or even earlier by testing embryos invitro if very early embryos are collected. The use of marker assistedgenetic selection will greatly facilitate and speed up cattle breedingproblems. For example, a modification of the multiple ovulation andembryo transfer (MOET) procedure can be used with genetic markertechnology. Specifically, females are superovulated, eggs are collected,in vitro fertilized using semen from superior males and implanted intoother females allowing for use of the superior genetics of the female(as well as the male) without having to wait for her to give birth toone calf at a time. Developing blastomeres at the 4-8 cell stage may beassayed for presence of the marker, and selection decisions madeaccordingly.

In one embodiment of the invention an assay is provided for detection ofpresence of a desirable genotype using the markers.

The term “genotype” as used herein refers to the identity of the allelespresent in an individual or a sample. In the context of the presentinvention a genotype preferably refers to the description of thepolymorphic alleles present in an individual or a sample. The term“genotyping” a sample or an individual for a polymorphic marker refersto determining the specific allele or the specific nucleotide carried byan individual at a polymorphic marker.

The present invention is suitable for identifying a bovine, including ayoung or adult bovine animal, an embryo, a semen sample, an egg, afertilized egg, or a zygote, or other cell or tissue sample therefrom,to determine whether said bovine possesses the desired genotypes of thepresent invention, some of which are indicative of improved reproductiontraits.

Further provided is a method for genotyping the bovine genes identifiedin Table 1, comprising determining for the two copies of the gene in adiploid genome present the identity of the nucleotide pair at therelevant SNP position (see below).

One embodiment of a genotyping method of the invention involvesexamining both copies of the gene, or a fragment thereof, to identifythe nucleotide pair at the polymorphic site in the two copies to assigna genotype to the individual. In some embodiments, “examining a gene”may include examining one or more of: DNA containing the gene, mRNAtranscripts thereof, or cDNA copies thereof. As will be readilyunderstood by the skilled artisan, the two “copies” of a gene, mRNA orcDNA, or fragment thereof in an individual may be the same allele or maybe different alleles. In another embodiment, a genotyping method of theinvention comprises determining the identity of the nucleotide pair atthe polymorphic site.

The present invention further provides a kit for genotyping a bovinesample, the kit comprising in a container a nucleic acid molecule, asdescribed above, designed for detecting the polymorphism, and optionallyat least another component for carrying out such detection. Preferably,a kit comprises at least two oligonucleotides packaged in the same orseparate containers. The kit may also contain other components such ashybridization buffer (where the oligonucleotides are to be used as aprobe) packaged in a separate container. Alternatively, where theoligonucleotides are to be used to amplify a target region, the kit maycontain, preferably packaged in separate containers, a polymerase and areaction buffer optimized for primer extension mediated by thepolymerase, such as PCR.

In one embodiment the present invention provides a breeding methodwhereby genotyping as described above is conducted on a bovine animal,especially a bull, and based on the results, certain cattle are eitherselected or dropped out of the breeding program.

Through use of the linked marker loci, procedures termed “markerassisted selection” (MAS) may be used for genetic improvement within abreeding nucleus; or “marker assisted introgression” for transferringuseful alleles from a resource population to a breeding nucleus (Soller1990; Soller 1994).

A method is further provided for determining whether an individualbovine animal is suitable as a gamete donor for natural mating,artificial insemination or in vitro fertilization, the method comprisingdetermining the identity of one or more SNPs according to the presentinvention using a method of the present invention, and excluding asgamete donor an individual which does not have the preferred alleleidentity at the respective SNP position as described in Table 1.

Specifically, an individual bovine animal, especially a bull, isexcluded as a gamete donor, if its genome does not have at least:

-   -   1) adenine (A) at the position of its MAP1B gene corresponding        to position 3066 of FIG. 1;    -   2) thymine (T) at the position of its MAP1B gene corresponding        to position 3323 of FIG. 1;    -   3) cytosine (C) at the position of its MAP1B gene corresponding        to position 87071 of FIG. 3;    -   4) guanine (G) at the position of its PPP1R11 gene corresponding        to position 112 of FIG. 4;    -   5) adenine (A) at the position of its DDX4 gene corresponding to        position 61646 of FIG. 6, or    -   6) G at the position of its DDX4 gene corresponding to position        34239 of FIG. 5.

In one embodiment, the individual is excluded as a gamete donor if thegene type of the individual is not homozygous of the preferred allelewith regard to the respective SNP position.

The present invention additionally provides a method of selecting abovine embryo for planting in a uterus, the method comprising genotypingthe embryo according to the present invention, while preserving theviability of the embryo, and excluding from planting an embryo whichdoes not have the preferred allele identity at the respective SNPposition as described in Table 1.

In another embodiment, the present invention further provides a methodfor selectively breeding cattle using a multiple ovulation and embryotransfer procedure (MOET), the method comprising superovulating a femaleanimal, collecting eggs from said superovulated female, in vitrofertilizing said eggs from a male animal which has at least onepreferred allele identity at the respective SNP position as described inTable 1 and above, implanting said fertilized eggs into other femalesallowing for an embryo to develop.

In another embodiment, the method for selectively breeding cattle usingMOET may further comprise a step of genotyping the male animal accordingto the method of the present invention.

In another embodiment, the method for selectively breeding cattle usingMOET may further comprise a step of genotyping the developing embryo,and allowing pregnancy to proceed only if the genotype of the embryocomprises at least one preferred allele identity at the respective SNPposition as described in Table 1.

The following examples are intended to illustrate preferred embodimentsof the invention and should not be interpreted to limit the scope of theinvention as defined in the claims.

Examples Materials and Methods

Associations of candidate fertility genes examined were carried out intwo experiments. In the first part, single nucleotide polymorphisms(SNPs) in the spermatogenesis genes were tested for associations withsire conception rate (SCR) in a large bull population. In the secondpart, genes found significantly associated with SCR were tested forassociation with female fertility traits (fertilization and blastocystrates). Male fertility genes that play roles in female fertility can beused to improve reproductive performance in cattle using geneticinformation from both males and females in breeding schemes.

Gene Selection, SNP Identification, and Genotyping for Bull Fertility

A total of 58 spermatogenesis genes, with conserved testicularexpression from fly to human, were reported in Bonilla and Xu (2008). Ofthose genes, only 22 were annotated in the bovine genome. For SNPidentification and genotyping, genomic DNA was extracted from semensamples of 268 Holstein bulls (Genex Cooperative/CRI, Shawano, Wis.)using standard phenol/chloroform protocols. One DNA pool was constructedfrom 20 random semen samples with equal amounts of DNA. The DNA pool wasamplified using primers designed in the 22 candidate genes to amplify 5′untranslated regions (UTRs), exons, introns, and 3′ UTRs. The PCRproducts were sequenced, and SNPs were identified by visually inspectingsequence traces. PCR amplification and sequencing were performed asdescribed in Khatib et al. (2008). Table 2 shows the primer sets used toamplify the nine candidate spermatogenesis genes found to be polymorphicin the bull population.

TABLE 2 Primers used to amplify the nine spermatogenic genes SEQ IDSEQ ID Product Gene Forward Primer NO: Reverse Primer NO: Size DCUN1D1ATACCCTTAGGCAGTTAG  7 AATTGTAAACCCTGAGAC  8 536 DDX4(1)AAACACGGAACAGAGGGT  9 AGGCAGGATTAGCAAGTATG 10 404 DDX4(2)AACCAAGTGGCTGGGATG 11 CAGACTCAAATGCGACAA 12 354 DNAI1(1)CGGTAAGTGAGCAGCATC 13 ACTGAAGCCTTTGCCCTA 14 495 DNAI1(2)CCCAGTGCTCCAAATCCT 15 ATGGCTCATCTTGTCTTCAGTA 16 413 DNAI1(3)CGTGACTGGGTTTAGGAT 17 CTGGTGGCTGCTGTCTAT 18 602 GAPDHS(1)CCAGGAAACGGCATCACC 19 ACACGCAGCAGGGCAACT 20 414 GAPDHS(2)GTGAAGGCCAGGGACTATGA 21 ACATGAACAAGAGGGCTGCT 22 541 GSTM3TTCTCTTCCCTGCAAGTCGT 23 TGAGAACAGCTGCCATCATC 24 664 MAP1B(1)CCATTTCCTAAGGCACAG 25 TTCCGCCATCTTCCTACA 26 504 MAP1B(2)CTTATGGTCGTGATTATGAA 27 AAGGCTAACACTGCTGGT 28 502 MAP1B(3)GGCTGTGACATACCTACC 29 CAGACCTTCCCTACTTATT 30 645 PPP1R11(1) CACATTACGGCGGAACTA 31 ATCCCAAGCAGTATCACCTA 32 591 PPP1R11(2)ACCTGTTCTATCTCCTCCCA 33 GTCACCTACCCACCTTGC 34 543 SPATA20TTGGAGAAGAAACCCACCAG 35 CCTCACAAGCAAGGCTAAGG 36 459 UBCTCGCTCAGTCGTGTCTTAC 37 TCAACCAACGCCTAATGT 38 420

A total of 24 SNPs located in the nine spermatogenic genes weregenotyped in the Genex population (268 animals) by MALDI-TOF MS(GeneSeek Inc., Lincoln, Nebr.).

Imputation of SNPs for Validation of Significant SNPs Found in GenexPopulation in a Larger Bull Population Obtained from the USDA

Solely for the purpose of validating the conclusions drawn from theresults using the Genex population, and to increase the sample size andimprove the statistical power of the study, the 24 SNPs identified inthe 9 candidate genes and genotyped in 268 bulls (from here forward, thereference population) were imputed in a total of 1,720 bulls (from hereforward, the imputed population) so that a final dataset of 1,988 bullswith genotypic data was generated for subsequent statistical analyses.Bulls in the reference and imputed populations have been previouslygenotyped with the Illumina BovineSNP50 Bead Chip, and hence shared SNPwere used to infer the genotypes of the unshared SNP in the imputedpopulation. Genotypes of the reference (n=268) and the imputedpopulations (n=1,720) for the 50K SNP Chip were provided by GenexCooperative/CRI (Shawano, Wis.) and the Animal Improvement ProgramsLaboratory of the United States Department of Agriculture (AIPL, USDA;Beltsville, Md.), respectively. SNP with minor allele frequencies below5% were removed. After data editing, 38,265 SNP spanning the entirebovine genome were available in both populations for the imputationprocess.

Imputation of SNPs was carried out for each candidate gene separately.In each case, a total of 100 SNP on each side of the gene were used toinfer the genotypes of the ungenotyped SNP. Imputation was performedusing the population-based haplotype clustering algorithm of Scheet andStephens (2006), which was implemented via the fastPHASE version 1.2software using the default settings for all parameters (University ofWashington TechTransfer Digital Ventures Program, Seattle, Wash.).

Phenotypic Data for Bull Fertility

The 1,988 bulls genotyped with the 50K SNP Chip were evaluated for sireconception rate (SCR), a phenotypic evaluation of bull fertilityprovided to dairy producers by AIPL-USDA as described in Peñagaricano etal. (2012). Briefly, SCR is the expected difference in conception rateof a sire compared with the mean of all other evaluated sires (Kuhn andHutchison, 2008; Kuhn et al., 2008).

In this study, SCR values ranged from −10.66% to +6.80%, and the numberof breedings per bull ranged from 303 to 111,402. SCR data were obtainedfrom seven consecutive evaluations provided by AIPL-USDA between August2008 and December 2010. For bulls with multiple evaluations, the mostrecent SCR evaluation was used in the analysis.

Statistical Analysis for Bull Fertility

The association between each SNP and SCR was evaluated using thefollowing mixed linear model,

SCR _(ijkl)=μ+EVAL_(j) +μSNP _(k)+sire_(i) +e _(ijkl)

where μ is the general mean, EVAL_(j) is the fixed effect of the j^(th)AIPL-USDA SCR evaluation (j=1, 2, . . . , 7), SNP_(k) is the number ofcopies of one allele of the SNP (corresponding to 0, 1 or 2 copies)carried by the i^(th) animal (i=1, 2, . . . , 1988), β is the regressioncoefficient for the SNP considered (also known as the allelesubstitution effect), sire_(l) represents the random additive geneticeffect of the l^(th) sire (l=1, 2, . . . , 246) of the i^(th) animal,and e_(ijkl) represents the random residual for each observation. Todetect possible deviations from the additive model, associations betweengenotype and SCR were evaluated using SNP as a categorical variable.

Random effects were assumed to follow the multivariate normaldistribution,

$( {{\begin{matrix}s \\ɛ\end{matrix}\sigma_{s}^{2}},\sigma_{ɛ}^{2}} ) \sim {N\lbrack {0,\begin{pmatrix}{A\; \sigma_{s}^{2}} & 9 \\0 & {W^{- 1}\sigma_{ɛ}^{2}}\end{pmatrix}} \rbrack}$

where s and ε are the vectors of sire and residual effects,respectively; σ_(s) ² and σ_(ε) ² are the sire and residual effectvariances, respectively; A represents the matrix of additiverelationships between sires in the pedigree (1,558×1,558) and W is adiagonal matrix of order 1,988 with its elements representingreliabilities of SCR values. The A matrix was calculated based on a.five-generation pedigree of sires downloaded from AIPL-USDA. Theassociation between each SNP and SCR was tested using a likelihood ratiotest by comparing to a reduced model without the SNP effect.

Phenotypic and Genotypic Data for Cow Fertility

The most significant SNP for SCR (rs109423562 located in MAP1B) wasfurther investigated for association analysis with fertilization andblastocyst rates—the main cow fertility traits—using an IVF system. Theprocedures of in vitro fertilization and subsequent embryo culture weredescribed in Khatib et al. (2008). To generate fertilization andblastocyst rate data, a total of 6,282 in vitro fertilizations wereperformed, and a total of 4,207 embryos were produced using oocytes from359 ovaries collected from 359 Holstein cows and semen samples from 12Holstein bulls. For 74 ovaries, oocytes were fertilized by two differentbulls each. Fertilization rate was calculated as the number of cleavedembryos at Day 2 post-fertilization divided by the total number offertilized oocytes collected from one ovary. Blastocyst rate wascalculated as the number of embryos that reached the blastocyst stage(Day 8) and appeared normal out of the total number of embryos produced.

The 359 ovaries were genotyped for SNP rs109423562 (G/A) using PCR-RFLP.A 171 bp fragment was amplified using the primers 5%GCAGCTCTTTTAGGAGTGTTAGCGTCTGAT-3′ (SEQ ID NO: 39) (forward) and5′-CTCACAGAGGGCATTTGACA-3′ (SEQ ID NO: 40) (reverse). The PCR productwas then digested by the restriction enzyme HinfI and electrophoresed ona 2.0% agarose gel. Allele G was cut while allele A was uncut.

Statistical Analysis for Cow Fertility

Association between SNP rs109423562 (G/A) in MAP1B and fertilization andblastocyst rates were analyzed using the following mixed linear model,

y _(ijk)=μ+ovary_(i)+sire_(j) +SNP _(ijk) +e _(ijk)

where y_(ijk) represents the fertilization or blastocyst rate of oocytek from ovary i fertilized with semen from bull j, μ represents a generalmean for the trait considered, ovary_(i) represents the random effect ofthe individual ovary from which oocytes were harvested, sire_(j)represents the random effect of the sire used in the fertilization,SNP_(ijk) represents the fixed effect of the ovary genotype for the SNPconsidered, and e_(ijk) represents the residuals, assumed normal,independent and identically distributed with mean 0 an variance Iσ_(e)². Ovaries and bulls were assumed uncorrelated with variance structuresIσ_(o) ² and Iσ_(s) ², respectively. Association between the SNP andfertilization or blastocyst rate was tested again using a likelihoodratio test by comparing with a reduced model without the SNP effect. Allthe statistical analyses were performed using the pedigreemm package(Vazquez et al. 2010) of the R language/environment (R Development CoreTeam 2009).

Results

SNP Identification and Association of Candidate Genes with SCR

Sequencing analysis revealed 24 SNPs in 9 spermatogenesis genes(DCUN1D1, DNA11, DDX4, GAPDHS, GSTM3, MAP1B, PPP1R11, SPATA20 and UBC)in the bull population using the pooled DNA sequencing approach. All 24SNPs located in 9 candidate genes were tested for association with sireconception rate first in Genex population and then in a largerpopulation of 1,988 bulls for validation.

Association Analysis in Genex Population

SNPs in the genes MAP1B, PPP1R11, and DDX4 are associated with SCR

For MAP1B gene, a SNP C/T in intron 5 at position 9331992 (University ofMaryland bovine version 3.1; UMD3.1) showed significant association withsire conception rate. Primers used to amplify the gene and SNP locationare shown in FIG. 1. Frequency of allele T was 25% and frequency ofallele C was 75%. The allele substitution effect was −0.15±0.01(p-value=0.01) so that allele C is favorable for SCR.

For PPP1R11, one SNP (T/G) in the 5′UTR region at position 28710268(UMD3.1) was significantly associated with SCR in the Genex population,with allele G associated with increased SCR. SEQ ID NO:6 shows SNPlocation and primers used to identify the SNP.

For DDX4, two SNPs located at positions 23382814 (SNP1; A/G) and23410221 (SNP2; G/A) were identified in the gene. For SNP locations seeFIG. 3. The two SNPs were in almost complete linkage disequilibrium, sothey have the same allele frequencies in the bull population examined.Genotype AA of SNP1 has 0.783 units of SCR versus −0.214 SCR units forGG genotype (P-value=0.05). Similarly, GG genotype of SNP2 has 0.749units of SCR versus −0.494 for AA genotype.

Association of Spermatogenesis Genes in the Combined Genex and USDAPopulations

Three SNPs located in MAP1B and one SNP in PPP1R11 showed significantassociations with SCR (Table 3). The SNP with the most significantassociation with SCR is SNP5.MAP1B located in intron 5 with an allelesubstitution effect of −0.24 and a P-value of 0.001. The other twosignificant SNPs were SNP1.MAP1B and SNP3.MAP1B, both located in intron1 with an allele substitution effect of 0.15 and P-values of 0.025 and0.039, respectively. After Bonferroni correction for multiple testing,only SNP5.MAP1B remained. significant (P-value=0.024). Pair-wise linkagedisequilibrium (LD) tests of MAP1B SNPs showed a moderate LD (r²=0.38)between SNP1.MAP1B and SNP3.MAP1B and SNP5.MAP1B. The LD betweenSNP3.MAP1B and SNP5.MAP1B was relatively low (r²=0.14).

SNP1.PPP1R11 located in the 5′UTR region of PPP1R11 showed significantassociation with SCR with an allele substitution effect of 0.15 and aP-value of 0.046.

TABLE 3 Genetic markers significantly associated with sire conceptionrate Allele Genotype substitution SNP ID Gene (N) effect ± SE P-valueSNP1.MAP1B MAP1B GG (463)   0.15 ± 0.01 0.025 GA (987) AA (538)SNP3.MAP1B MAP1B CC (972)   0.15 ± 0.01 0.039 CT (847) TT (169)SNP5.MAP1B MAP1B CC (1081) −0.24 ± 0.01 0.001 TC (763) TT (144)SNP1.PPP1R11 PPP1R11 TT (1033)   0.15 ± 0.01 0.046 TG (821) GG (134)

Association of MAP1B with Fertilization Rate and Embryo Survival Rate

SNP5.MAP1B located in intron 5 of MAP1B showed the most significantassociation with sire conception rate in the bull population analyzedabove. To characterize its impact on female fertility, we tested theassociation of this SNP with fertilization rate and blastocyst rate inthe IVF system. SNP5.MAP1B showed significant associations with bothfertilization rate (P-value=0.027) and blastocyst rate (P-value=0.029)(Table 4). Oocytes collected from genotype CT cows showed the lowestfertilization rate (59.9%) compared with that from CC (66.4%) and TT(66.3%) cows (Table 4). For blastocyst rate, the CT genotype againshowed the lowest rate (27.1%) while homozygous CC and TT individualsshowed blastocyst rates of 31.0% and 41.8%, respectively (Table 4).

TABLE 4 Association between SNP5 of MAP1B gene and fertilization rateand blastocyst rate Genotype Fertilization rate Blastocyst rate (N)Estimate ± SE P-value Estimate ± SE P-value CC (321) 0.664 ± 0.03 0.0270.310 ± 0.02 0.029 CT (84) 0.599 ± 0.03 0.271 ± 0.03 TT (28) 0.663 ±0.04 0.418 ± 0.05

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1-22. (canceled)
 23. A method for implanting an embryo comprising: invitro fertilizing cattle eggs to obtain fertilized eggs, culturing thefertilized eggs into developing embryos, i) detecting the identity of anucleotide of a MAP1B gene of an embryo at a position corresponding toposition 1986 of SEQ ID NO: 1, wherein the MAP1B gene comprises thenucleotide sequence of SEQ ID NO:1, and identifying an embryo that hasan adenine at said position, or ii) detecting the identity of anucleotide of a MAP1B gene of an embryo at a position corresponding toposition 2243 of SEQ ID NO: 1, wherein the MAP1B gene comprises thenucleotide sequence of SEQ ID NO:1, and identifying an embryo that has athymine at said position, or iii) detecting the identity of a nucleotideof a PPP1R11 gene of an embryo at a position corresponding to position232 of SEQ ID NO: 3, wherein the PPP1R11 gene comprises the nucleotidesequence of SEQ ID NO:3, and identifying an embryo that has a guanine atsaid position, or iv) detecting the identity of a nucleotide of a DDX4gene of an embryo at a position corresponding to position 2006 of SEQ IDNO: 4, wherein the DDX4 gene comprises the nucleotide sequence of SEQ IDNO:4, and identifying an embryo that has an adenine at said position, orv) detecting the identity of a nucleotide of a DDX4 gene of an embryo ata position corresponding to position 2139 of SEQ ID NO: 5, wherein theDDX4 gene comprises the nucleotide sequence of SEQ ID NO:5, andidentifying an embryo that has a guanine at said position, andimplanting into a suitable female bovine said identified embryo.
 24. Amethod for selecting a bull bovine animal as a breeder, the methodcomprising: (1) performing a procedure selected from the groupconsisting of: i) obtaining a sample of the animal's nucleic acid,wherein the nucleic acid comprises at least a partial MAP1B genecomprising SEQ ID NO:1, detecting an adenine nucleotide at a position ofthe MAP1B gene of the animal corresponding to position 1986 of SEQ IDNO: 1, selecting the bull bovine animal that has an adenine at saidposition, or ii) obtaining a sample of the animal's nucleic acid,wherein the nucleic acid comprises at least a partial MAP1B genecomprising SEQ ID NO:1, detecting a thymine nucleotide at a position ofthe MAP1B gene of the animal corresponding to position 2243 of SEQ IDNO: 1, selecting the bull bovine animal that has a thymine at saidposition, or iii) obtaining a sample of the animal's nucleic acid,wherein the nucleic acid comprises at least a partial PPP1R11 genecomprising SEQ ID NO:3, detecting an guanine nucleotide at a position ofthe PPP1R11 gene of the animal corresponding to position 232 of SEQ IDNO: 3, selecting the bull bovine animal that has a guanine at saidposition, or iv) obtaining a sample of the animal's nucleic acid,wherein the nucleic acid comprises at least a partial DDX4 genecomprising SEQ ID NO:4, detecting an guanine nucleotide at a position ofthe DDX4 gene of the animal corresponding to position 2006 of SEQ ID NO:4, selecting the bull bovine animal that has an adenine at saidposition, or v) obtaining a sample of the animal's nucleic acid, whereinthe nucleic acid comprises at least a partial DDX4 gene comprising SEQID NO:5, detecting an guanine nucleotide at a position of the DDX4 geneof the animal corresponding to position 2139 of SEQ ID NO: 5 selectingthe bull bovine animal that has a guanine at said position, and (2)using bovine cell or tissue from the identified bull animal in abreeding procedure.
 25. A method according to claim 24, wherein thebovine cell is a sperm.
 26. A method according to claim 24, wherein thenucleotide is detected by sequencing the MAP1B gene or a relevantfragment thereof.
 27. A method according to claim 26, wherein the geneor a relevant fragment thereof is isolated from the animal's nucleicacid sample via amplification by a polymerase chain reaction of genomicDNA of the cell.
 28. A method of claim 23, wherein the identity of bothcopies of the gene in the cell is determined.
 29. A method according toclaim 23, wherein the nucleotide is detected by sequencing the gene or arelevant fragment thereof.
 30. A method according to claim 29, whereinthe gene or relevant fragment thereof is isolated from the animal'snucleic acid sample via amplification by a polymerase chain reaction ofgenomic DNA of the cell.
 31. A method of claim 24, wherein the identityof both copies of the gene in a cell is determined.